A passenger (name unknown) exits a Northbound train at Bayshore station on Wednesday, April 6, 2011. Bayshore station at 400 Tunnel Road in San Francisco will be closed as part of Caltrain's funding plan requiring fare increases without service cuts.

Photo: Anna Vignet, The Chronicle

A passenger (name unknown) exits a Northbound train at Bayshore...

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A Northbound train pulls into Bayshore station on Friday, April 6, 2011. Bayshore station at 400 Tunnel Road in San Francisco will be closed as part of Caltrain's funding plan requiring fare increases without service cuts.

Buoyed by its ability to raise enough money to avoid gutting Caltrain, the commuter railroad's Board of Directors voted Thursday to put off a vote on budget-balancing service cuts for two weeks and try to find another $3.5 million to keep running its current 86-train schedule.

Caltrain is enjoying record ridership, carrying about 41,000 passengers each weekday, and has seen increases in weekend patronage. But the agency lacks a dedicated funding source, and is dependent on contributions from SamTrans, the Santa Clara Valley Transportation Authority and the San Francisco Municipal Transportation Agency. All three agencies are struggling with their own budget woes and have reduced their payments, which are determined by formula.

Until this week, it looked as if Caltrain would have to eliminate all but 48 morning and evening commute trains, curtail service to Gilroy and stop serving 16 stations to slash $30 million from its $103 million budget. But the transit agencies and the Metropolitan Transportation Commission cobbled together enough money to run a 76-train schedule that keeps all-day, weekend and special service, but eliminates the popular Baby Bullet trains and closes three stations, including Bayshore in Brisbane and Capitol in San Jose.

Dozens of Caltrain riders expressed relief at staving off the draconian cuts but urged the board not to trim service at all, saying it would discourage transit ridership and development near the railroad's stations.

"You cannot do this," said Bill Hedges, a developer building a transit-oriented development near the Hayward Park Station, which trains would bypass under the plan. "This sends the wrong message."

Director Adrienne Tissier, a San Mateo County supervisor, agreed, and called for the two-week delay to try and rustle up enough money to avoid the cuts altogether.

"Ridership is up, on-time performance is up, (fare revenues) are up," she said. "This is not a broken system. But we are going to break it. The Baby Bullet is what made Caltrain successful."

All of the directors agreed to the delay but some said they were concerned that balancing the budget on one-time funds would create an even bigger challenge finding money for the 2013 budget.

"We all want to see a robust service," said Director Omar Ahmad. "Any cuts are vile. But we have to put together a service that is sustainable."